<div dir="ltr">Hello,<div><br></div><div>I am trying to run the khmer/sandbox/filter-below-<wbr>abund.py script in order to trim off high-abundance kmers for a metagenome assembly.</div><div><br></div><div>Below is the command I want to run:</div><div><span style="color:rgb(51,51,51);font-family:monospace,monospace;font-size:12.8px;white-space:pre-wrap">python /local/cluster/khmer-legacy/</span><span style="color:rgb(51,51,51);font-family:monospace,monospace;font-size:12.8px;white-space:pre-wrap">sa<wbr>ndbox/filter-below-abund.py </span><span style="color:rgb(51,51,51);font-family:monospace,monospace;font-size:12.8px;white-space:pre-wrap">4B_hostfilt_count </span><span style="color:rgb(51,51,51);font-family:monospace,monospace;font-size:12.8px;white-space:pre-wrap">4B_norm_hostfilt.fq --cutoff 50 -T 5 -M 100</span></div><div><span style="color:rgb(51,51,51);font-family:monospace,monospace;font-size:12.8px;white-space:pre-wrap"><br></span></div><div><span style="color:rgb(51,51,51);font-size:12.8px;white-space:pre-wrap"><font face="arial, helvetica, sans-serif">The </font></span><span style="color:rgb(51,51,51);font-family:monospace,monospace;font-size:12.8px;white-space:pre-wrap">4B_hostfilt_count</span><span style="color:rgb(51,51,51);font-size:12.8px;white-space:pre-wrap"><font face="arial, helvetica, sans-serif"> file is the countgraph file created via </font><font face="monospace, monospace">load-into-counting.py</font><font face="arial, helvetica, sans-serif"> and the </font></span><span style="color:rgb(51,51,51);font-family:monospace,monospace;font-size:12.8px;white-space:pre-wrap">4B_norm_hostfilt.fq </span><span style="color:rgb(51,51,51);font-size:12.8px;white-space:pre-wrap"><font face="arial, helvetica, sans-serif">file is sequence file after normalization (</font><font face="monospace, monospace">normalize-by-median.py</font><font face="arial, helvetica, sans-serif">).</font></span></div><div><font color="#333333" face="monospace, monospace"><span style="font-size:12.8px;white-space:pre-wrap"><br></span></font></div><div><font color="#333333"><span style="font-size:12.8px;white-space:pre-wrap"><font face="arial, helvetica, sans-serif">And this is the error I receive:</font></span></font></div><div><span class="gmail-m_2951284255394044883gmail-im" style="font-size:12.8px"><p class="gmail-m_2951284255394044883gmail-m_-8987188898056572026gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal"><span class="gmail-m_2951284255394044883gmail-m_-8987188898056572026gmail-s1" style="font-variant-ligatures:no-common-ligatures"><font face="monospace, monospace">Traceback (most recent call last):</font></span></p></span><p class="gmail-m_2951284255394044883gmail-m_-8987188898056572026gmail-p1" style="font-size:12.8px;font-variant-numeric:normal;font-variant-east-asian:normal;margin:0px;font-stretch:normal;line-height:normal"><span class="gmail-m_2951284255394044883gmail-m_-8987188898056572026gmail-s1" style="font-variant-ligatures:no-common-ligatures"><font face="monospace, monospace"><span class="gmail-m_2951284255394044883gmail-m_-8987188898056572026gmail-Apple-converted-space"> </span>File "/local/cluster/khmer-legacy/s<wbr>andbox/filter-below-abund.py", line 49, in <module></font></span></p><p class="gmail-m_2951284255394044883gmail-m_-8987188898056572026gmail-p1" style="font-size:12.8px;font-variant-numeric:normal;font-variant-east-asian:normal;margin:0px;font-stretch:normal;line-height:normal"><span class="gmail-m_2951284255394044883gmail-m_-8987188898056572026gmail-s1" style="font-variant-ligatures:no-common-ligatures"><font face="monospace, monospace"><span class="gmail-m_2951284255394044883gmail-m_-8987188898056572026gmail-Apple-converted-space"> </span>main()</font></span></p><p class="gmail-m_2951284255394044883gmail-m_-8987188898056572026gmail-p1" style="font-size:12.8px;font-variant-numeric:normal;font-variant-east-asian:normal;margin:0px;font-stretch:normal;line-height:normal"><span class="gmail-m_2951284255394044883gmail-m_-8987188898056572026gmail-s1" style="font-variant-ligatures:no-common-ligatures"><font face="monospace, monospace"><span class="gmail-m_2951284255394044883gmail-m_-8987188898056572026gmail-Apple-converted-space"> </span>File "/local/cluster/khmer-legacy/s<wbr>andbox/filter-below-abund.py", line 22, in main</font></span></p><p class="gmail-m_2951284255394044883gmail-m_-8987188898056572026gmail-p1" style="font-size:12.8px;font-variant-numeric:normal;font-variant-east-asian:normal;margin:0px;font-stretch:normal;line-height:normal"><span class="gmail-m_2951284255394044883gmail-m_-8987188898056572026gmail-s1" style="font-variant-ligatures:no-common-ligatures"><font face="monospace, monospace"><span class="gmail-m_2951284255394044883gmail-m_-8987188898056572026gmail-Apple-converted-space"> </span>ht = khmer.load_counting_hash(count<wbr>ing_ht)</font></span></p><p class="gmail-m_2951284255394044883gmail-m_-8987188898056572026gmail-p1" style="font-size:12.8px;font-variant-numeric:normal;font-variant-east-asian:normal;margin:0px;font-stretch:normal;line-height:normal"><span class="gmail-m_2951284255394044883gmail-m_-8987188898056572026gmail-s1" style="font-variant-ligatures:no-common-ligatures"><font face="monospace, monospace">AttributeError: 'module' object has no attribute 'load_counting_hash'</font></span></p><div><span class="gmail-m_2951284255394044883gmail-m_-8987188898056572026gmail-s1" style="font-variant-ligatures:no-common-ligatures"><font face="monospace, monospace"><br></font></span></div><div><font face="arial, helvetica, sans-serif"><span style="font-variant-ligatures:no-common-ligatures">I am concerned that I am getting this error because the filter-below-abund.py script is no longer part of the khmer pipeline. </span></font></div><div><font face="arial, helvetica, sans-serif"><span style="font-variant-ligatures:no-common-ligatures"><br></span></font></div><div><font face="arial, helvetica, sans-serif"><span style="font-variant-ligatures:no-common-ligatures">The newest installed khmer in our linux /local/cluster/bin is version </span></font><span style="font-size:12.8px">2.0+103.g8300de0, but the filter-below-abundance.py script did not show up after the installation.</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">The script I used came from an older installation of khmer in /local/cluster.</span></div><div><span style="font-size:12.8px"><br></span></div><div>(The python version I am using: <span style="font-variant-ligatures:no-common-ligatures"><font face="monospace, monospace">Python 2.7.14,</font><font face="arial, helvetica, sans-serif"> and the OS Version: </font></span></div><div><span style="font-variant-ligatures:no-common-ligatures"><font face="monospace, monospace">Linux 3.10.0-693.11.6.el7.x86_64 x86_64</font></span><font face="arial, helvetica, sans-serif" style="font-variant-ligatures:no-common-ligatures">)</font></div>
<div><span style="font-variant-ligatures:no-common-ligatures"><font face="arial, helvetica, sans-serif"><br></font></span></div><div><span style="font-variant-ligatures:no-common-ligatures"><font face="arial, helvetica, sans-serif">I wanted to know if anyone would know why I am getting this error, if the filter-below-abund.py script should be included in installations of the latest khmer version, and if this script is still functioning.</font></span></div><div><span style="font-variant-ligatures:no-common-ligatures"><font face="arial, helvetica, sans-serif"><br></font></span></div><div><font face="arial, helvetica, sans-serif"><span style="font-variant-ligatures:no-common-ligatures">Thank you,</span></font></div><div><font face="arial, helvetica, sans-serif"><span style="font-variant-ligatures:no-common-ligatures">Adriana Messyasz</span></font></div>
<div><br></div>-- <br><div class="gmail-m_2951284255394044883gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><a href="http://vegathurberlab.oregonstate.edu/people/adriana-messyasz" target="_blank">Adriana Messyasz</a><div>Ph.D. Student</div><div>Vega Thurber Lab</div><div>Oregon State University</div><div>Corvallis, OR 97331</div><div>email: <a href="mailto:messyasa@oregonstate.edu" target="_blank">messyasa@oregonstate.edu</a></div></div></div></div></div></div></div>
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